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Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia
This dataset contains the results from a metabarcoding study of terrestrial leech blood meals to detect differences in the diets of two leech species, Haemadipsa picta and Haemadipsa sumatrana. Mammal taxa were identified using metabarcoding of 16s rRNA and comparisons of operational taxonomic units (OTUs) to a curated reference database from NCBI (National Center for Biotechnology Information) GenBank. All leeches were collected from the Stability of Altered Forest Ecosystems project (SAFE; www.SAFEproject.net) as part of the NERC Human Modified tropical Forest Programme and the LOMBOK consortia (Land-use Options for Maintaining BiOdiversity & eKosystem functions). Leech samples were collected at different sites across a habitat gradient, to assess these invertebrates as molecular sampling tools for mammals. Individuals were pooled before amplicon sequencing with Illumina MiSeq 150-200bp x2. The resultant raw sequences were filtered and clustered at 97%, curated and then assigned to the reference database using BLAST and MEGAN programmes. Full details about this dataset can be found at https://doi.org/10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
Simple
- Date (Publication)
- 2018-08-08
- Citation identifier
- https://catalogue.ceh.ac.uk/id/3affed0d-fe6f-4916-89e3-e672639191e5
- Citation identifier
- doi: / 10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
- Other citation details
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Drinkwater, R., Schnell, I.D., Bohmann, K., Bernard, H., Veron, G., Clare, E., Gilbert, T.P., Rossiter, S.J. (2018). Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia. NERC Environmental Information Data Centre 10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
- Point of contact
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Organisation name Individual name Electronic mail address Role Queen Mary University of London Drinkwater, R.
Point of contact Queen Mary University of London Drinkwater, R. Author Natural History Museum of Denmark
Schnell, I.D. Author Natural History Museum of Denmark
Bohmann, K. Author Universiti of Malaysia Sabah Bernard, H.
Author Muséum national d'Histoire naturelle Veron, G. Author Queen Mary University of London Clare, E. Author Natural History Museum of Denmark
Gilbert, T.P. Author Queen Mary University of London Rossiter, S.J.
Author NERC EDS Environmental Information Data Centre Custodian NERC Environmental Information Data Centre Publisher
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Wikidata
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GeoNames
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- Other restrictions
- Other constraints
- no limitations
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If you reuse this data, you should cite: Drinkwater, R., Schnell, I.D., Bohmann, K., Bernard, H., Veron, G., Clare, E., Gilbert, T.P., Rossiter, S.J. (2018). Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia. NERC Environmental Information Data Centre https://doi.org/10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
- Spatial representation type
- Text, table
- Distance
- 150 urn:ogc:def:uom:EPSG::9001
- Language
- English
- Character set
- UTF8
- Topic category
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- Biota
- Begin date
- 2015-02-01
- End date
- 2015-06-30
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- Unique resource identifier
- WGS 84
- Distribution format
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Name Version Comma-separated values (CSV)
- Distributor contact
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre
Distributor
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/data/3affed0d-fe6f-4916-89e3-e672639191e5 Download the data
- OnLine resource
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Protocol Linkage Name https://data-package.ceh.ac.uk/sd/3affed0d-fe6f-4916-89e3-e672639191e5.zip Supporting information
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- Dataset
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dataset
Conformance result
- Title
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Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
- Date (Publication)
- 2010-12-08
- Statement
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Individuals of both species were collected at 25m2 vegetation plots in the forest blocks (A-F, LFE, LF1-3 & VJR) at the SAFE project Sabah (corresponding to second order points). Plots are approximately 173m apart and all plots were sampled 4 times between February 2015 and June 2015. Sampling consists of searching the leaf litter and undergrowth for leeches for a fixed time of 20 minutes. Individuals are kept in RNALater to stabilise DNA until extraction. DNA extraction of pools of ten individual leeches was undertaken using a digestion buffer with modified QiaQuick (Qiagen) protocol and dual tagged PCR in triplicate reactions (details in Drinkwater et al. in review). After screening samples for successful PCR amplification, a total of 41 samples of pooled Haemadipsa sumatrana and 49 pooled Haemadipsa picta from six sites remained for sequencing (B, F, D, LF, LFE, VJR). Amplicons were pooled for library build following Carøe et al, 2017) and sequencing with Illumina MiSeq 150-200bp x2. Sumaclust was used for OTU clustering (Mercier et al., 2013) and LULU was used for post-clustering filtering (Frøslev et al., 2017). This resulted in the final contingency table comparing mammal detections with leech pool. Carøe, C., Gopalakrishnan, S., Vinner, L., Mak, S. S. T., Sinding, M. H. S., Samaniego, J. A., Wales, N., Sicheritz-Ponten, M., Gilbert, M. T. P. (2017). Single-tube library preparation for degraded DNA. Methods in Ecology and Evolution, 9(2), 410-419. https://doi.org/10.1111/2041-210X.12871 Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188. https://doi.org/10.1038/s41467-017-01312-x Mercier, C., Boyer, F., Bonin, A., & Coissac, E. (2013). SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. In Programs and Abstracts of the SeqBio workshop (pp. 27-29).
Metadata
- File identifier
- 3affed0d-fe6f-4916-89e3-e672639191e5 XML
- Metadata language
- English
- Character set
- 8859 Part 1
- Hierarchy level
- Dataset
- Hierarchy level name
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dataset
- Date stamp
- 2025-11-13T16:16:24
- Metadata standard name
- UK GEMINI
- Metadata standard version
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2.3
- Metadata author
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Organisation name Individual name Electronic mail address Role NERC EDS Environmental Information Data Centre Point of contact
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